Yep, that how they are supposed to sit. There's a drain in there that often gets blocked though, it takes water down to the triangle louvered part at the end of the window. There's a few bits of advice somewhere here on the forum I think, but inter webs may be able to help if the search function here doesn't give you an answer.
They windows and drainage tubes are a bit different for t-tops and hardtops, but they all stand away from the body the was shown in your pic.